Things were Different
by ranma-tomoe
Summary: up for adoption, Msg me for details. What if Rei wasn't the first experiment
1. The beginning

                              Things were Different

DISCLAIMER: I do not own anything that has to do with NGE they belong to GAINAX and the creator of the series, of course. With that said, let's get on with the fic.  Ok, the first part of this fic pretty much  stays true to the real story line except that a few things have been altered. Basically, I took some of the things that I thought would be interesting. I'll give reasons at the end of every chapter/ part.  well I'm going to get started. Oh, this story is based mainly on the three pilots and the main cast. I will have parts with the bit cast.but not big parts. note, this is an alternate universe fic. and Yui Ikari does not exist in this universe, so Gendos maiden name will be Ikari. all will be explained in time for those of you who are wanting to argue.oh and the attacks don't happen in the exact order as they do in the series. Oh I do own one character. Those of you who have read my zoids fic will know who it is._update: 07/20/02_  I am seriously thinking about making this a crossover fic, with the ZOIDS universe…(very original, ain't it…)

    CHAPTER 1:   THE BEGINNING

 DISCLAIMER: I do not own anything that has to do with NGE they belong to GAINAX and the creator of the series, of course.

'---------' = thoughts

"---------" = speech

                           Ikari, Shinji was at a pay phone in the pouring rain. Luckily it was a booth phone, he pulled out a piece of paper that had a picture of a dark haired woman  with a note on the bottom, 'I will meet you at the designated area that is on your id card.' It also had a phone number at the end of the note.  Shinji picked up the phone and dialed the number. 

"I'm sorry but all lines are are out of order due to special circumstances." Shinji looked at the phone as he put it back on the base. He merely sat and waited for captian Katsuragi to come pick him up. after twenty minutes went by he noticed a rather large monster walking towards Tokyo three. Even though it was a ways away it looked close. But Shinji stayed expressionless. He heard screeching coming from the corner of the street, and a car coming, seemingly at full speed. As if a professional was driving it came to a screeching halt, right in front of the booth. The woman from his picture stepped out of the car, and ran through the rain to meet him. 

"How are you Shinji-kun?" asked a drenched Misato Katsuragi. 

"I am fine,captain Katsuragi-san." was all he said, not even a thank you. 'He acts alot like Rei, a little spooky.' Misato thought. When Misato looked at the angel she noticed a n2 mine dropping down on top of it. 

"HIT THE DECK!!!" Captain Katsuragi shouted as she pulled Shinji down with her, as she noticed he didn't react fast enough for her taste. After the blast subsided, she made sure that her, 'cargo', so to speak, was alright and then, she and Shinji got the car pushed back over,and started for the geo-front. While driving somewhat recklessly she got a phone call. "Yes he is, his safety is my top priority. I will take full responsibility for this." and hung the phone up.  

"Katsuragi-san?" Shinji asked in an emotionless voice as he looked straight ahead. 

"What is it, Shinji-kun?" Misato asked, noticing another disturbing similarity to Rei Ayanami. 

"What is my purpose? before now, I have had no purpose. I would like to know what makes me useful." Shinji said remaining emotionless but now looking at Misato.

 "I can't tell you that yet Shin-kun, but I will as soon as I am able."Misato answered, wanting to tell him, but knowing she couldn't. 

"I can accept that." Shinji answered looking at the rain falling on the windshield again. 

She made another phone call on her cell phone. "Yes, where is the nearest car transport train?... Good, that's right near us, have them prep it. We're on our way." Misato looked at Shinji, 'He acts so unnattached for some reason. I'll have to ask him about that if we get out of this attack alive.' Misato thought, as they head on to the transport car of the train. It is secured, and they start heading for the geo-front. 

"Do you have the id card that your father sent you?" Misato asked going in to military mode, somewhat.

 "Yes, it is right here, do you need it?" asked a expressionless and monotonous Shinji.  'This is starting to freak me out, the only differences between him and Rei are gender and he talks a little louder than Rei.' Misato thought as she answered him. 

"No, you just needed it so I could give you this." Misato hands Shinji a sealed folder that read "welcome to NERV" He read through it and set it down as they came to a stop at the geo-front. As they walked, Misato commented at how beautiful this place was. 

"It is what it is." Shinji stated as he walked without looking at anything. By now, saying Misato was annoyed at the boy's attitude was a very big understatement, but she just grinded her teeth as they made their way to the eva cages. One Ritsuko Akagi-san met them as they were walking to the elevator. 

"You're late, Misato! And time is not on our side." Ritsuko-san proceeded to chew Misato out when the alarms went off. "Is this the boy?" Ritsuko-san asked. 

"Yes, this is Shinji Ikari..." Misato said, waiting for him to introduce himself. "Shinji, say hello to Dr. Akagi."  

"Hello Dr. Akagi-san." Shinji said, looking at Ritsuko-san with an emotionless face on. Misato motioned for Shinji to get on the elevator and wait for herself and Ritsuko-san. 

"He acts almost exactly like Rei." Misato said as she looked towards Shinji. 

"He acts like he is still in a state a trauma induced shock from one or more past incidents, it might be temporary or it could be permanent. Only time will tell." Ristuko-san stated. And the two women got on to the elevator, unaware that Shinji could read lips. He was not pleased with them talking about him, but what he felt didn't matter. The only thing that mattered was doing what he was told. 

                   Misato, Risuko-san and Shinji entered the cages for the EVA's. Shinji wondered why it was so dark, and as if to answer his question lights came on to reveal the face of EVA 01. Most people would be frightened by this sight, but Shinji only stared at it. To Misato's amazement he said, "This is my purpose, to pilot this." as if he knew ahead of time. 

"Why is unit 01 being prepped? Rei is not in any condition to pilot." Misato sounded angry. 

"She will not have to pilot, Shinji will pilot it." Gendo said as he looked at Shinji.

 Misato broke in before Shinji could accept or refuse, "You expect us to have Shinji pilot when it took seven moths just to get Rei synched with it!?" 

"We can only try, if he can not synch and pilot it, we will use Rei." Gendo said with a little aggravation in his voice. He did not like insubordination in his ranks. 

"I accept the offer, commander, I will attempt to take out the enemy." Shinji said looking at his father but still held no emotion in his voice. 

"Captain Katsuragi, show him to the entry plug." Gendo ordered. 

"Yessir." Misato said, grabbing Shinji by the hand. Misato grumbled unintelligable words as she led Shinji to the plug. As they walked to the plug Misato asked, "Why would you want to pilot something that you have had no training for?" 

Shinji answered, "As I said before, before today I have had no purpose, and father has given me a purpose." and walked on to the entry plug.  

"Shinji, once you get inside, the plug will fill with a liquid called 'link connection liquid' or LCL for short, it helps yu breathe as well as helps you pilot the eva. Oh, here put these on. these allow you to connect with the EVA. Once inside I will continue to explain, is that understood?" Misato said, as she handed him the head piece. 

"Understood." Shinji answered, still in a monotonous voice. While back on the command bridge, the commander, Gendo Ikari, sat in his chair overlooking the majority of the command bridge. A figure stepped out of the shadows. 

"Do you think he will be able to synch with 01, much less pilot it?" the figure asked. 

"Yes, I have not been completely out of reach with the second childs development. I figured from the beginning he would pilot what I created, so I had him unknowingly trained for this, note how he is as subordinate as Rei." Gendo said, with a little pride in his voice. 

"So, you have planned for this?" the figure asked as he looked on while Misato continued to explain the basic controls of the eva. 

"I always think ahead. Shinji will also be the second part that the prophecy talks of, we have already acquired the DNA samples of what was left of Adam. Now all we need to do is to re-engineer the second child's DNA with that of Adam's and simply follow the same procedure we did with Rei. Then our scenario will be certain, and thanks to nano-technology I can activate the Adam and Lillith cells in each of them when I wish." Gendo explained. 

"You have thought of everything, Gendo" the figure stated. 

"Don't I always, Kozou." Gendo answered and then the figure, known as sub-commander Kozou Fuyutsuki, stepped back into the shadows.

After Shinji had went over the controls with Misato one more time, they proceeded to start the  synchronization process. after absolute thesh hold is crossed they see that his synch ratio is at 78.2%. 

"It's incredible! I've never seen a synch ratio this high from a rookie, especially for some one who never even got into an EVA before." Maya stated. 

"Captain, the angel is directly above NERV." Shigeru reported. 

"Launch EVA!" Misato ordered, and under her breath, she whispered, "Come back to us Shin-kun."

END CHAPTER 1 : THE BEGINNING

 author's notes: First off an n2 mine is like a nuke without the harmful side effects, notice in the beginning of the chapter, how the two people felt the shockwave from where they were, and it was a pretty fair ways from the angel. I have not decided about any pairings in this fic. I was leaning towards a Shaya 

( Shinji/Maya) pairing but thought about with his new personality defect what it would be like if I had a Reinji (Rei/Shinji) fic. yah, yah, I know it would be sort of like incest, but they don't know that and I claim poetic rights or something like that. I have no idea what it means but it sounded cool when I read it. well I will get on to the next chapter. I'm 10-7 for now.


	2. First Battle

CHAPTER TWO : THE BATTLE 

DISCLAIMER: I do not own anything that has to do with NGE they belong to GAINAX and the creator of the series, of course.

'---------' = thoughts

"---------" = speech

           "Launch EVA!" Misato ordered, and under her breath she whispered: "come back to us, Shin-kun." As soon as the EVA reaches the surface they release the final safety lock, Misato tells him to concentrate only on walking. He stumbles at first and then gets his bearings but not in time to avoid the hand lunging for his left arm. " Shinji, open your left shoulder panel and use yur proggressive knife to get free." Misato ordered. 

"Hai." Shinji said through gritting teeth. Just as he gets the prog knife out the angel snaps the bone on the giant eva. Shinji shouts in pain, but still carries out his mission. He slashes the angel across the chest, revealing a giant red orb, which he nicked. The angel, angry at what the EVA had done, picks him up by the head and throws him into a couple buildings. Unknown to Shinji, people still inhabited the buildings, not that it would have made much difference to him, as he was not ordered to watch out for civilians. Before Shinji could get up, the angel, again, picked him up by the neck and proceeded to beat him in the skull. after about thirty seconds of beating Shinji is unconcious due to shock, and the techs are going crazy. 

"Brain casing cracked, it can't take much more of this." one tech shouted, and another shouted, "We have a problem, I can't get any pilot readings!"  And then the Angel self destructs. An average sized crater is left and a significantly damaged unit 01. Gendo did not look happy but did not look unhappy either. 

"I think given the situation he did pretty well." Fuyutsuki commented. 

"I agree, but if I had brought him in sooner he would not have caused as much damage to unit 01, or to the surrounding area. I also would like to know why the angel self destructed like that." Gendo observed. When they got the hatch of unit 01's entry plug open, they took Shinji to the infirmary, to check for any contamination. After Dr. Akagi-san finished her tests, Shinji left to find captain Katsuragi. Either unknown to him, or he just didn't care, Ritsuko-san had taken more than just tests, she had gathered DNA from him,which was, in this case, a single hair, and took it to a specimen dish in the back of the tent, and starts studying how the hair is affected by what's in the dish. 

"Commander will be very pleased with these rsults." Ritsuko-san said almost jumping for joy.  Shinji walked outside the room, and even though he didn't let it show he was ashamed of himself. 

"I failed at the only purpose I was given. I will not fail again." Shinji said in a voice that was almost emotionless except for the shame. About that time, Misato came up. 

"Have you gotten your living arrangements in order?" she asked. 

"No, I have not." Shinji said in his regular monotone voice. 'Boy he is got to get out more.' Misato thought. Maya showed up about thirty seconds later. 

"Excuse me, commander Ikari wants to see Shinji." Maya said, as she motioned for Shinji to come with her. Shinji stood there waiting for Misato to confirm this. 

"It's alright, go with her." Shinji did as he was instructed. While Shinji was going to see his father, Misato decided to taked it upon herself to read up on his history. In the commanders office, Shinji stood in front of Gendo, waiting for the reason he was called here. 

"Shinji, tell me why you voluntarily piloted something that could have gotten you killed." Gendo ordered, testing the limits of Shinji's loyalty to him. 

"I was instructed to, by you. Do you not remember?" Shinji asked still not showing any emotion, in his voice or on his face. 

"No, I remember, but I what I want to know is your reason for piloting the EVA, and not just because you were ordered to." Gendo said, as if trying to find something. 

"Until now I have had no purpose to anyone or anything, but after you called me I knew there was a purpose that I could finally have. I have had no real reason for existing in this world, That is why I pilot, and if not for anything else, I pilot for you in appreciation for giving me a purpose in life." Shinji said. Shinji actually surprised himself. That was the most he had talked in the past eight years that he could remember. 

"Shinji, I have a few things I would like to go over with you. First, your new living quarters will be in block six. In addition, I want you to start taking self defense lessons, you will go to them right after your school day is over, the lessons are only an hour long. After that, you will have free time." Gendo said. 

"Hai." Shinji answered. 

"I will have your things moved there immediately." Gendo said. 

"That will not be necassary, I only have a music device, and six sets of clothes. They are in captain Katsuragi's car, and as for self defense, I am well versed in ju-ditsu, but if you still wish me to, I will go to these classes." shinji said still monotonous. Gendo nodded, in confirmation. 

"Then that will be all, you may return to captain Katsuragi now." Gendo said motioning for Shinji to leave. After Shinji left the room the shadowy figure of sub-commander Fuyutsuki stepped out of the shadows. 

"He will follow orders as blindly as Rei?" asked Fuyutsuki. 

"Yes, as you heard he... appreciates me for giving him a purpose. Has dr. Akagi finished her tests yet?" Gendo asked. "Yes, his DNA will nicely conform to Adams DNA. Then we can clone him as well. We are lucky to not have had to replace the original Rei Ayanami." Fuyutsuki said not speaking to any one in particular. 

"Yes, there is a better chance of succeeding with the original two." Gendo added. 

"When will we start the procedure?" Asked Fuyutsuki. 

"I will let you know when I have decided." Gendo answered. And with that Fuyutsuki melted into the shadows once more.

++++

"Captain Katsuragi-san, may I get my things out of your car? I am going to my new living quarters." Shinji said. 

"Are you sure that's what you want to do?" Misato asked, not entirely sure he should be left alone. 

"It is what the commander ordered, so I have to comply." Shinji stated. 

"We'll see about that" Misato said under her breath. After a heated debate, well a one sided heated debate with the commander, she finally got him to let Shinji stay with her. 

"Well, that went over better than I expected it to." Misato said to no one in particular. "Now to find Shinji and tell him the good knews.

'why does ms. Katsuragi-san seem to care about me so much? She seems to act different when  referring to me when I'm not around. She keeps comparing me to some one named Rei. Maybe I will ask her. Father, he is an enigma to me as well. he seems interested in me but for a different reason. I know he thinks a lot of me but as to why, I have no idea. From what I can understand, he called on me for no reason at all. I wonder, if I open up to both of them what the result would be.'  Shinji thought as he waited for the elevator to come back down where a tech had used it before, he assumed. That's where Misato found him. 

"Hey, Shin-kun, I got some good news. You get to live with me! Isn't that great!" Misato said, trying to at least get some type of emotion out of this boy. 

"Is this cleared with the commander?" Shinji asked, still emotionless. 

Misato shrugged her shoulders and said "Yes, I cleared it with him. Now let's go to your old apartment and get some of your things." 

"All of my belongings, are in my duffel bag." Shinji answered, getting into the elevator. 

"You mean everything you own is in that bag!?" Misato shouted, not believing that a teenager had so few things. After they finally make it to Misato's apartment, Misato forgot where she put her Key card. After about five minutes, she finds it and opens the door. 

"Ojamashimasu?"Shinji asked. 

"Hey, Shin-kuuuun, remember it's your house now too." Misato called from her bath room. Shinji walked into the living room, and saw what looked like a tornado after math. Beer cans, whiskey bottles, and sake bottles all over the floor. As if on cue Shinji proceeded to pick up the beer cans, and etc. By the time Misato got changed and walked in to the living room, Shinji had half of her mess cleaned up. "Shinji, you didn't have to clean up, you know." Misato commented. Shinji continued to clean up the mess. After Shinji got through cleaning the mess up, he went to his duffel bag, picked it up, and asked Misato where his room would be. She pointed it out to him and he went in to his room. He settled his things on the desk in that room, although his posessions weren't many. They consisted of a SDAT player, a couple tapes, as well as some books that he liked to read, as well as five pair of formal school clothes and a pair of slacks, red tee-shirt and a cap. He picked up one of the books and started reading, when Misato knocked on his door. 

"Yes, Katsuragi-san?" Shinji asked in his monotonous voice. 

"First off, call me Misato, next I want to know, what your preferred meals are." Misato said. To Shinji it sounded like an order, so he answered it as such.

"I do not have a preferrence in food, Katsuragi-san." Shinji answered. 

"I said call me Misato when we're off duty! That's an order." Misato shouted, but was playing about the order part. 

"Yes, Misato-san" Shinji answered again, this time answering the way Misato wanted. As Misato was leaving, Shinj called her. 

"Misato-san." "Yes, Shin-kun?" Misato asked. 

"I apologize if I made you angry, I am not used to dealing with people. The people I have gotten close to have either died or left. So, as you can see I am not accustomed to people making a preference as to what I call them." Shinji said in a monotone voice. 

"I see, well that's changed now. I am going to be your 'parent' from now on." Misato tried to get closer to him, trying to get him to open up. 

"May I ask you something, Misato-san?" Shinji asked. 

'He's starting to open up to me.' she thought, "Yes, ask any thing you want." She answered, confident she could answer his question. 

"Why do you talk nice to me when I'm around, but talk bad about me when you think I can't hear you?" he asked. 

". . . . . ." Misato opened her mouth, trying to answer, but nothing would come out. 'How could he have heard mine and Rit-chan's conversation?' And as if to answer her mental question, Shinji said "If you're wondering, I can read lips. If you want to speak about me, please learn english. That is one of the languages I have not learned yet."  

Finally Misato could talk, "Shinji, Dr. Akagi and I  were talking about your mental condition, I thought you had went through some trauma earlier in your life. and she thought so as well." Misato said, trying to defend her actions. 

"If you have questions about me, ask me, I am not permitted to lie to a superior officer, per the commander's orders." Shinji said still in his monotonous voice. 

"If he asked you to jump off a cliff would you?" Misato asked, getting more than a little mad at this boy. He just sat there a minute, not answering, then said "Yes, if he ordered it." Misato walked off muttering something about a male version of this Rei he was starting to hear about all the time. Shinji started packing his things. 

'I must in some way have angered her in some way, it would be best if I was to go to the designated apartment to live.' he thought. As he was finishing packing his things he heard a squawk at his door. He turned to see what it was, and found a black and white penguin, with a red looking streak of hair on his head. Misato came to the door scolding the bird, and noticed Shinji packing. 

"Where are you going, Shin-kun?" She asked. 

"I am going to the designated apartment I was assigned to. It seems that I am not doing anything other than angering you." Shinji answered. Even though he had told her the truth, she was his guardian now and would be held responsible, but more than that it hurt her feelings to have him think that she was another person that was going to abandon him. 

"Shin-kun, I order you to stay here." She said, hoping he would take it as a military order. He did. She hated doing that, it made her feel like a slave master. "Shinji, why do you follow orders so blindly?" Misato asked. 

"Because I have been taught to follow orders, and so, I do as ordered." he answered. 

"Whatever, I'm going to go to bed. You have synch tests, and training tomorrow. and the day after that, you start school, so you need to get your rest." Misato said. and left Shinji to unpack once more.

END CHAPTER TWO : THE BATTLE

author's notes.   Ojamashimasu - may I come in.

                             well I was primarily trying to give some background information in this chatpter, but only got to touch on it. I will further the background info in little increments with different characters I still haven't decided on whether or not to make this a Maya/Shinji or a Rei/Shinji fic.so I will get in to that later after I get someone better associated with the series to help with the overall writing. I am looking for an eva fan pre-reader, sorry ayame. maybe on one of my final fantasy fics.Well I'm 10-7 for now.


	3. Consequences of Battle

CHAPTER THREE : THE CONSEQUENCES OF THE FIRST BATTLE

 DISCLAIMER: I do not own anything that has to do with NGE they belong to GAINAX and the creator of the series, of course.

'---------' = thoughts

"---------" = speech

""---------""= computer talk

      At the training simulator, Shinji was doing particularly well for his first try. After about two hours of tests, that he passed without trying hard, lunch time arrived. He walked around the complex, over the past year or so he found he could eat less than most people and still have the sufficient energy to work. While he was walking around, he walked into lt. Maya Ibuki. He asked if he hurt her. 

"I'm alright, what about you?" asked Maya. Shinji was taken aback by what she asked him. 

'This total stranger is concerned about me. This is something I am not accustomed to.' Shinji thought as he nodded, and walked on. 

Maya giggled a little bit, then sighed. "I don't think he knew how to react to kindness."  After lunch break was over Shinji headed back to the locker room. When he turned the corner, he saw Ritsuko-san waiting for him. 

"Am I late, Dr. Akagi-san?" Shinji asked hoping he hadn't angered her. 

"No, you are not late, but I need you to come with me to the commander's office." Ritsuko-san answered. 

"Hai." Shinji complied. As they waked to Gendo's office Shinji turned his head to face Ritsuko-san. 

"Dr. Akagi-san, why do you think I am still in a state of shock induced trauma?" he asked bluntly but still held no emotion in his voice. 

Unlike Misato, Ritsuko-san handled this with elegance. "It's because not many children your age have the same attitude that you have, unless they went through some very bad trauma." 

"You are correct, but trauma induced personality changes don't last as long as my personality has." Shinji countered. Ritsuko-san knew he was right. 

"I have one more question. Who is Rei? I have been compared to her many times." Shinji asked. 

"My, aren't we full of questions today? Well Rei is the pilot of unit 00, the prototype model evangelion, and the reason we were comparing her to you, is that she acts alot like you." Ritsuko-san answered two questions, one he yet to ask. "Well here we are. After you." Ritsuko-san said as she motioned for him to enter. After they got in there Ritsuko-san personally gave Gendo the reports on the tests that she did on Shinji's chance of compatilbility with merging him with the Adam cells. Shinji for the most part, just stood there, looking out one of the windows, at the geo-front forest, seemingly unaware of the conversation that had to do with him. Gendo called him, which got his full attention on the spot. 

"Sir?" He answerd as he was supposed to. 

"In the near future I will call on you to participate in a project. You are to cooperate in any way you are able. Is that understood?" Gendo ordered. 

"Hai." Shinji answered. 

"How is your meds? They sould be getting low, right?" Gendo inquired. 

"Yes, but I do not know where to get them filled." Shinji responded. 

"That's fine, Dr. Akagi will give you the needed medications." Gendo said as he scribbled down some med names on a piece of paper, and handed it to Ritsuko-san. 

"That is all, you may leave now." Gendo said waving them off. As the pair walked to her office to get the meds, she noticed that these were the same meds given to Rei, to suppress her emotions. 

"So, it isn't trauma induced…" She said aloud. Shinji ignored her, looking straight ahead. The rest of the day went as scheduled, with the exception that Shinji finished the training a little earlier than expected. He was walking around, waiting for Misato to get off shift, he made his way to the infirmary. He walked down the halls, for some reason, something in an open door caught his eye, he looked in, and saw a girl with blue hair was sleeping. He looked at the door and saw that it had Ayanami, Rei on the folder, in the holder. 

'So this is the Rei I have been compared to so much.' he thought. He continued his walk. Misato finally got off her shift, and she and Shinji went home. On the way home, she asked 

"So how did your tests and training go today? I had to go meet someone on an American ship, so I missed them." Misato asked. 

"According to Dr. Akagi-san, they were satisfactory. I believe I heard lt. Ibuki say that they were remarkably high." Shinji answered in a monotonous voice.

"Those meds are the same that you give Ayanami, aren't they?" She asked, she knew the answer but wanted to hear it from him. 

"Yes, why do you ask?" He inquired. 

"I would like to know why you are giving them to him." Ritsuko-san answered. 

"Simple, it would serve me better to have both subjects to be submissive to my orders rather than objective. You agree, don't you?" Gendo said, in his usual cold tone. 

"I agree." Ritsuko-san said, not totally believing how ruthless this man could be. 

"Is that all?" He asked.

"Yes, that is all." Ritsuko-san said leaving Gendo's office.  By this time Misato and Shinji have made it back to their place. 

When Misato walks in she shouts "TADAIMA!" Shinji walks in and goes straight to his room and puts his meds in his drawer, after he takes some. After a horrible dinner, Shinji asked if he could cook from now on. Misto immediately agreed. 

"You should get ready to go to bed, it's getting late, and you have school tomorrow." The next morning, when Misato got up, it was 5:30,and  she found Shinji had already prepared both of their breakfasts as well as his lunch for the day. and he was getting out of the shower. 

"Talk about an early bird." Misato said remembering what the person on the ship said, when she got off the helicopter, looking drowsy. After Shinji had gotten his clothes on, he ate his breakfast. "You sure are up early, aren't you Shin-kun." Misato said looking at Shinji who was now reading a book. 

He never looked up from the book, and answered, "I do not want to be late for school." 

"You want a ride to school?" Misato asked, trying once again to get close to her charge. 'I'm starting to think this was a bad idea.' Misato thought. 

"I...would like that, Misato-san." Shinji said, thinking that would be a good place to start his little experiment. Inside Misato was jumping for joy. 

'I think I'm starting to get him to open up to me.' She thought. Misato took him to his new school, and went back to her place. Shinji went in to the class room he was assigned to and the teacher showed him where to sit. After he got settled in to his new seat, he noticed that blue haired girl he saw in the infirmary, she still had bandages on various parts of her body but she could at least walk., and do some activities. Shinji was taking down notes as the teacher instructed the class to do, when his laptop made a sound, and an instant message appeared. 

""Are you the pilot of the giant robot? Y/N"" 

Shinji replied ""I can not say, that is classified."" and then half of the class gathered around him. Everyone except the blue haired girl he knew was Rei. She continued to stare out the window. The teacher got the children to settle down and give Shinji some much wanted space.When lunch time got there, Shinji finished his lunch, and proceeded to go back to the class room. When he got near the class room, two boys called him in to one of the closets. The more muscular one swung at Shinji. Luckily, Shinji had taken ju-ditsu lessons while he was with his last guardian / teacher, and deflected his attack and twisted the boys arm around his back, and pushed him against the wall, and kicked the other boy, in the stomach, making him double over. 

"Why did you try to attack me?" Shinji asked in his monotone voice. 

The boy that was doubled over wheezed out, "He talks like the ice princess." Shinji asked one more time, putting more pressure on the boy's arm. 

"AAAGHHH, I have to hit you, I won't be satisfied until I do." He managed.  The boy that was doubled over had since gotten his breath back and was standing next to Shinji. 

"I do not understand." Shinji said, trying to figure out why some stranger would want to harm him for no reason. 

"You have to look at it from his point of view. You see, his sister was in one of the buildings that collapsed the day the angel attacked. She lived but was injured and needs special care." the boy explained. 

"I...did not know that. I am sorry that your sister was injured, but it could not be helped. I was not aware of, nor advised to watch out for civilians." Shinji stated as he let go of the other boy. As soon as he let the other boy go he turned and planted his fist in Shinji's temple, and knocked him against the wall, and slid to the floor. 

After Shinji stood up looking unphased by the blow, he said, "Does that help ease your grief?" and walked out of the room and in to the class room. The only sign he had been hit was the red mark on his fore head. 

"He sure does act like that Rei girl doesn't he?" the boy with glasses said.

"He is a jerk, Kensuke, and yes he does act a lot like Rei, but he is a little more decisive than she is, maybe a little, but not very much." said the boy who attacked Shinji. 

"I don't know, Touji, he has the same lifeless expression that she has. and I noticed something else about them both. They look like they could be related." Kensuke said. 

The rest of the school day went perfectly. no disruptions and, by the time the class bell rang Shinji had a stack of notes that stood a good three inches. On his way to Misato's apartment, he caught a glimpse of the two boys following him. Shinji jogged in to an alley, waitng for them to follow. They did. Shinji stepped out of his hiding spot, right behind them. 

"Why are you following me?" he said in his monotone voice. That, added to the fact that the alley was already scary looking made them jump pretty high. 

"How did you do that!?" Kensuke asked more out of amazement than fear or anger. 

"Why are you two following me?" Shinji asked again in the same voice. 

"I wanted to apologize to you, I was a little rude." Touji answered. Shinji cocked an eyebrow, and continued to look at Touji. "Ok, more than a little rude. I apologized, now you can hit me." Touji continued. 

"I see no need to hit you." Shinji answered. 

"Uhhh, I was.. Well we were wondering if we could come to your place and hang out." Kensuke said,butting in, as he rubbed the back of his head. 

"I think we got off on the wrong foot, and we were wanting to try to get to know you better to try to understand the reason what happened, happened to my little sister." Touji finished. Shinji stood there about a minute in silence. 

"Most of what you want to know is classified, but I will help in any way I can." He finally said. Kensuke and Touji gave the victory sign as they gave each other five. Misato was gone when Shinji got there. There was a note on the table. 

It said, "Shin-kun, I have gone to NERV on some buiseness. Do your chores and when I come in, I will inform you on what you and I will be doing tomorrow." Shinji went about his chores making sure his company was comfortable. After he got through he sat on the floor facing the sofa that Kensuke and Touji sat on. 

"You said you had some questions to ask me." Shinji said, again in his usual monotone voice. 

"Well the first question is, what were you doing when you were piloting that thing?" Touji asked, sarcasm evident in his voice. 

"Following my orders, take out the enemy. The only other thing about that I can tell you is that it was my first time piloting it." Shinji said, still no emotion in his voice. 

"I see, so basically, what happened was beyond your control? I thought that pilots for eva were trained years in advance." Kensuke thought aloud. Mistake, Shinji made a mental note to inform the commander of the information that Kensuke had. They talked, well Kensuke and Touji asked questions in which Shinji answered as best he could without divulging any classified information, or talking much. 

"I think it's about time to leave Kensuke, it's about five o'clock and I have to get to the house." Touji lied, he was getting tired of the company he was in. 

"I think that we should go as well, I have some... things to do." Kensuke said. After the company left, he called commander Ikari and informed him of the situation. 

"Keep an eye on them and inform me if either of them find out any classified information you think would jeapordize our project, and don't let captain Katsuragi know of this, understood?" Gendo ordered. 

"Hai." Shinji answered. About that time, Misato swipes her key card through the slot and unlocked her door. She entered and found Shinji putting the reciever back on the base. 

"Got friends already?" Misato asked a smile on her face. 

"Wrong number." Shinji answered.  

Misato only shrugged her shoulders and sighed, "Well you and I have a parent teacher conference tomorrow. Something about you beating a kid up."  

"I acted in self defense, the other person attacked first." Shinji answered. 

"Oh, and do you know who it was?" Misato asked. 

"Yes, it was Suzuhara, Touji. He and his friend just left, you might have seen them while you were coming up to the room." Shinji answered.

END CHAPTER THREE : THE CONSEQUENCES OF THE FIRST BATTLE

A.N.. Again, I have not decided on which way the romance thing would go. I may make a split off from the start of the romance thing, making a side story for the other fans of which ever one I pick. Like if I choose a rei/shinji pairing I'll make a split off from the original story and write with the other pairing to please the other fans. I may just make it an asuka/ shinji pairing, with Rei as his 'sister' well I still have no pre-reader so if any eva nut wants to help I would appreciate it. well I'm heading to bed now, oh and I'm sorry that some of these chapters seem long, I sit at home all day with nothing to do, and I come up with ideas for this story. I know I said it would stick to the main story line, but I just couldn't, I had too many good ideas and not enough brain space, so I started writing them on the screen and it fit perfect with the mood and everything. well I'm getting sleepy, I know this because I only ramble when I'm sleepy. well I'm 10-7


	4. First Real Battle

CHAPTER FOUR : FIRST REAL BATTLE

DISCLAIMER: I do not own anything that has to do with NGE they belong to GAINAX and the creator of the series, of course.

'----------' = thoughts

"---------" =speech

Two weeks later. "Pattern Blue confirmed." Maya reported. 

"Get unit 01 ready, where's the pilot?" Misato asked, as she continued to give orders. 

"He'll arrive in T-minus 4 minutes; section two agents are escorting him here." a Aoba reported. 

"Good, will unit 01 be ready when he gets here?" Misato asked, wanting to end this quickly. 

"Yes, it will be ready by the time pilot Ikari has changed in to his plug suit." Maya again answered. 

"What about pilot Ayanami? Is she able to pilot?" Misato asked looking at Ritsuko-san. 

"Yes, but her Eva is not and full combat capacity enough for battle yet." Ritsuko-san answered. Ritsuko-san was nervous about the second child's safety, she had not collected enough DNA samples to sufficiently clone him. 

"The pilot is ready to launch." Makato reported. 

"How long until unit 00 is ready to launch?" Misato asked ignoring Makato who announced unit 01 was ready. 

"Two hours at best." Maya reported. 

"Very well, Launch unit 01!" Misato ordered. 

"High intensity energy build up in the target!" shouted one of the techs monitoring the angel. 

"Shinji! Move!" Misato shouted. Shinji moved as fast as he could but it wasn't fast enough. His right arm, up to his shoulder as well as part of his right leg were incinerated by the blast. 

"AAAAAAAAIIIIIIIIIIIIIIYYYYYAAAAAAAAAA!!!!" screamed Shinji as he was hurled backwards by the force of the impact to his arm. Even though she only knew him for a few weeks, Misato was near tears, watching Shinji go through this pain. Misato had wanted Shinji to show emotion, but not like this. 

"Shinji, can you walk?" Misato asked trying not to sound overly worried. 

"Hrrrrhhh, I.... I'm alright....I, I will complete my... mission." Shinji managed between sucking in LCL through clenched teeth. By sheer will and determination, he stood the Eva up on both feet and headed for the nearest ammo building, clutching a stub that used to be his Eva's right arm, and limping very badly. 

"Shinji, abort mission, return to base." Misato ordered. 

"Not that I am questioning your motives, but why are you recalling unit 01? You are still aware that in commander Ikari's absence I am in charge, are you not?" Fuyutsuki asked Misato. 

"Yes, I am aware of that, but if Shinji is lost in this battle, we will not have any viable option left to use against the angel." Misato said as she prepared to meet Shinji in the infirmary. 

"I am not disagreeing with your actions, I was merely trying to make sure you understood who was in charge here. You have a habit of forgetting that." Fuyutsuki said. 

"I don't have time to get in to this right now, I have to check on pilot Ikari." Misato said, leaving the bridge, Ritsuko-san hot on her heels. "Why are you coming with me? I thought you were supposed to be checking on the Eva." Misato questioned. 

"Shinji is a higher priority to the operation than the Eva." Ritsuko-san said, following Misato in to the hospital wing. 

"Shin-kun? Are you awake?" Misato asked. 

"I am awake, Misato-san." Shinji said as emotionless as ever. "I am sorry, I have failed my mission once again." Shinji said now looking at his commanding officer, and roommate. 

"No one could have dodged that blast entirely, Shinji. I was amazed that you were able to avoid more damage than was incurred." Ritsuko-san cut in. 

*Misato snaps her finger*

"Ritsuko is right, and I think I have an idea of how to destroy the angel. I will be back, I have some things to do." Misato said, leaving the room. Ritsuko-san took this chance to get the rest of the DNA that she needed. As she was getting ready to draw some blood, she told Shinji that this was for the operation; the one that Gendo had spoken of, and for him not to talk about this. He agreed. After Ritsuko-san got the sufficient blood she needed, she left. Shinji rested while he waited for his next orders. After a few minutes passed by, he heard somebody at his door, though it was very faint. "Yes?" he inquired, his eyes closed. 

"I wanted to see if you were still able to pilot." Rei said in a voice that was similar to his own tone, emotionless and blank. 

"I am able to pilot, I am just in shock from the damage to the Eva. It will subside in time for me to pilot again." Shinji said. 

"Why do you act as I do?" Rei asked. 

"I don't know. I have acted this way since I can remember." Shinji answered, not knowing why, but answering anyway. 

"And you, pilot Ayanami, why do you act as you do? Most people our age seem to act... 'normal' as Captain Katsuragi calls them." Shinji asked. 

Rei was not immediately able to answer that question. "I...do not know either. Like you I have acted as I do ever since I can remember." Rei answered, like Shinji, she did not know why she answered. 

"Pilot Ayanami, I would like to continue conversations like these, would you mind?" Shinji asked, feeling like she would understand him. 'I wonder if this is the feeling called trust?' Shinji mentally asked. 

"I would also." Rei answered. 

"I have things to attend to but we will continue this conversation another time." Rei said as she left. Five minutes later, Misato came in and informed Shinji of her plan. 

"When I left, I went to the command bridge, to find out some things and one of the techs said that a close range combat was impossible. That reinforced my idea. So I commandeered a prototype positron rifle, and we are going to use it to destroy the angel." Misato explained. After she explained the details of the operation, she and Shinji went to the cages. "Your unit is still damaged, but it will be a simple operation. All you have to do is hit the core, it is showing on the chest of the angel. Rei will be your backup." Misato said as Shinji sat in his entry plug. 

"I will not fail this time, Misato-san." Shinji said. Misato only sighed at how determined he was to prove his worth. When Misato got back to the bridge, Maya reported that both Evas were ready to launch. While Misato was giving orders, Ritsuko was talking to Fuyutsuki. 

"The angels are attacking out of order, we were expecting a different angel than this one." Ritsuko informed. 

"I believe they are getting smarter. As we are seeing now." Fuyutsuki said. 

"Just as well, we were starting to win to easily anyway." Ritsuko joked. 

"Launch units 00 and 01!" Misato ordered. When the Evas reached the surface, Rei had to help Shinji to the rifle. After the rifle was charged, Shinji put the angel in his sights. 

"I have the target in my sights, advise when to fire command." Shinji reported. 

"Fire when you feel you have a good shot." Misato said as she sat down in her chair. After he thought he had a good bead on the angel he fired. 

"DIRECT HIT!!" said Maya who was monitoring Shinji's weapons systems. On the way down Shinji wanted to talk to his father, so he established a connection to the commander's personal viewer. Instead of Gendo, it was Fuyutsuki that answered. 

"Where is Commander Ikari, Sub-commander Fuyutsuki?" Shinji asked, monotonous as usual. 

"He had a meeting to attend." Kozou Fuyutsuki answered. 

"Inform him that I wish to see him." Shinji requested. 

"He will be informed." Kozou said. 

"Thank you." Shinji said as he was helped to his cage. 

"Shinji, Rei, excellent work." Misato said as she readied for the debriefing.

END CHAPTER FOUR: FIRST REAL BATTLE 

A.N. I should have ended the chapter sooner but I just couldn't. I turned 18 a couple days ago and my parents haven't quit nagging me to go to college, for those of you who care I am going to college but I have to finish all of my fics right now. I might start the romance in the next chapter, although I might go into some more vague character history. I think you will find it takes a twist. Oh I am going to introduce Asuka in a different way this time. She won't be on the ship; that will be another character. She will be introduced in the next couple of chapters. Well I am going to shut the computer down for now. It has been some very bad weather, and I am risking my computer's safety to make sure I get down these ideas. Well I am going to get a notebook, and continue the story. 10-7.

p.s. one question, what do you think would happen if one very blunt person asked another ver blunt person a very personal question? Find out in the next chapter.


	5. Realizations

CHAPTER FIVE : REALIZATIONS

DISCLAIMER: I do not own anything that has to do with NGE they belong to GAINAX and the creator of the series, of course.

'-------------' =thoughts

"------------"= speech

(Three days later.) 

"The commander will see you now." said a secretary looking person. Shinji got up, and walked in to the commander's office. 

"You wanted to see me?" Gendo asked. 

"Yes." Came the monotone reply. 

"What did you want to speak to me about?" Gendo asked again. 

"I...have things I need you to explain to me." Shinji said. 

"What kind of things?" Gendo asked. 

"I wish to know who my mother was. And explain what a mother is like, so I can better understand captain Katsuragi. She is becoming an enigma to me." Shinji said. 

"Well, a mother provides care for her children. She tries to teach them things they need to know to survive, as well as comforts them when the children are feeling sad." Gendo tried to explain. The only person, before now, he had to explain such things to… was Rei. So he was a little under experienced for this kind of stuff. 

"That is sufficient. I have one more question, why are you keeping me in the dark about your project? I wish to know about such things, since they include me, if it is alright with you." Shinji said. He knew something was going on, but he didn't know what. 

"If you want to know, follow me." Gendo said, as he got up and left the room. Shinji obediently followed. Shinji was taken to a lab, where there were tanks that held something in them but he could not tell what at first. 

"You wish to know the truth? Here it is." Gendo said as he pointed to one of the tanks. Shinji walked to the tank and looked in it. What he saw didn't outwardly affect him, but on the inside he was screaming. 'What am I!?!?!?!?'. "I made you because my parents wanted a grandson. But by the time I had completed you, they had both died, so I left you with a college professor, that was a good friend of mine. But I still kept tabs on you, because you were the first clone I had made. I had him train your mind to pilot EVA, as I knew you would have to pilot it someday. After I left you with my friend, the company I worked for wanted me to create another person the same way. So you are the original children." Gendo explained. 

"I... understand." Shinji said. Still not showing any emotion. "But, there is something I do not understand, to create a human life you need DNA from both a male and female. Who was the female?" Shinji asked. 

"It was an anonymous donor." Gendo answered, "Why do you want to know? You shouldn't worry about that, all you need to know is that you were genetically engineered, and that you have only one purpose." Gendo said. 

"Hai." Shinji answered. 

After they went back to Gendo's office, Gendo said, "You may talk to Rei about this if you wish, she was also genetically engineered. Anyone else you tell will be put out of the picture. You may leave now." Shinji left, and went straight to the EVA cages. For some reason, it seemed to calm him some, maybe it was the fact that they were artificial, like him. 

After about an hour or two, Misato came and got him. "Why were you down there?" Misato asked. 

"I can not tell you, it is too classified." Shinji said in a monotonous voice but had a little twinge of sorrow in it. 

"I am going to leave, do you need anything of me before then?" Shinji asked. 

"No, I suppose that will be all. What time will you be home?" Misato asked, not really paying attention, because she couldn't get over the fact that he had classified information that she didn't. 

"I do not know." Shinji answered. 

"Be home before twelve midnight." Misato said. 

"Hai." Shinji answered, and left Misato thinking. 'I don't think I will ever understand him.' she thought to herself, and walked off, to try to find out what the information was. Shinji walked around until he was satisfied that Rei was not at NERV, he looked up her address on the MAGI super computers. He got the address and left to talk to Rei. He had to talk to someone and his fa...the commander said he could talk to Rei about it. As he walked up to Rei's door, for some reason, he felt worried. 'What if she does not know of her origins?' he thought, then another thought occurred to him. 'Why am I worried about Rei?' Shinji asked as he rang her doorbell. The greeting from the other 'special' child pulled him from his reveries. 

"Pilot Ikari? Are you alright?" Rei asked looking at him with a curious look on her face. 

"I...was just thinking." Shinji said, emotionless, but still blushed a little, and honestly not knowing why. 

"Do you wish to talk?" Rei asked. 

"Yes. You said we could talk, earlier." answered Shinji. 

"Do you wish to come in?" Rei asked. 

"Yes." he answered. After they go in to her apartment, they started talking. 

******

"Do you know where you came from? Like who your mother is?" Shinji asked. 

"I was genetically engineered, to pilot EVA, but I suppose I have a mother." Rei said, lowering her head just a little bit. 

"You were genetically engineered as I was." Shinji thought aloud. This got Rei's attention. 

"You were genetically engineered?" Rei asked, surprise evident in her voice. 

"Yes, I was just informed of it today." Shinji answered. 

"Then it won't be long..." Rei said offhandedly. 

"Until what, pilot Ayanami?" Shinji asked finally showing some emotion. 

"I can not tell you that yet, but I can tell you that you will never be the same." Rei said. 

"I can accept that." Shinji answered. The two teens talked until 11:30 that night, about different things. Some about her, and some about Shinji. They both found that they enjoyed the conversation and decided to continue these conversations. 

"I have to go, it has been... an enjoyable experience." Shinji said, as he left Rei at her door. 

"It has." Rei answered to herself. 

"Pushing it weren't you?" Misato asked sarcastically. 

"I was here before the designated time." Shinji answered, walking into the bathroom, to get a shower. 

"Well you have a synch test tomorrow, you aren't required to attend school on that day, so if you wish you don't have to go. That means you can sleep in." Misato said walking in to the bathroom, getting toothpaste and tooth brush out to brush her teeth. 

Shinji thought for a couple of minutes. "I will attend school." Shinji answered as he proceeded to get undressed, to get a shower. The fact that Misato was in there with him didn't seem to bother him, as it did her. 

"I AM IN HERE TOO YOU KNOW!!!" Misato shouted as she left with toothpaste foam in her mouth. 

"You walked in while I was getting ready for a shower." Shinji answered. Misato continued to rant about how ill mannered he was while he was getting his shower and seemed to worsen when he got out, to face her. Shinji couldn't help but smile a little. 

"WHAT'S SO DAMN FUNNY!?" She asked still very much pissed. 

"You look like a rabid beast." he said, still emotionless, but still smiling a little 

"I am glad you are showing emotion, but do you have to show it at my expense?" Misato asked looking for a mirror. 

"Gomen, Misato-san." Shinji said handing her a small mirror. 

As soon as she looked at herself in the mirror, she busted out laughing. "I didn't know I looked that funny!?" she said between gathering air. 

"I am going to bed. I'll get a shower tomorrow." Shinji said as he went in to his room, after he got decent. 'Today has been eventful. I have found I can openly talk to Rei, and Katsuragi-san and I are starting to form a sort of understanding.' Shinji thought, genuinely smiling for the third time tonight. 

********

(The next morning.) Shinji had gotten up at is usual time of 5:00 in the morning and had gotten ready for school and made breakfast and was on the couch reading while he ate a piece of toast. Misato walked in and stared at the table. 'I don't think I am ever going to get used to this.' She thought. 

"Shinji, you are going to spoil me rotten." Misato said as she dug in to her food. Shinji just kept on reading. After Misato had eaten she sat down beside Shinji who still had a piece of toast in his mouth while writing something down. "Whatcha writin' Shin-kun?" Misato asked while trying to see. 

"It is nothing. By the way, your alcohol consumption has impaired your work efficiency, I checked up on you, and you have been going to work intoxicated recently so I discarded your beer." Shinji said. Well half of it was true she had been drunk, but not enough to impair her judgement any, he just found that the smell of beer made him sick, and for some reason he did not want anyone, especially Misato to know. 

"YOU WHAT!!!?" Misato screamed, as she ran to the fridge to find that her beer was gone. 

"Don't try to buy any either, you won't be able to. I went to commander Ikari and he has forbidden any liquor stores to sell beer to you." Shinji said. 

Misato had a look of pure death in her eyes as she approached Shinji, ready to beat the living tar out of him, when the doorbell rang. "Saved by the bell, Ikari." Misato said, as Shinji went to answer the door. 

Rei was waiting on the other side of the door. "Pilot Ayanami? Why are you here?" Shinji asked. 

"I am here to escort you to Dr. Akagi's lab, She requested our presence early today." Rei said, a monotonous as ever. 

"Why was I not informed of this?" Misato asked finally calming down enough to talk rationally. 

"I just found out this morning my self, Captain Katsuragi-san, so I assume, it is spur of the moment." Rei said. 

"I will be ready in about five minutes." Shinji said as he went to put his personal things out of Misato's sight. He took the notebook he was writing on with him, to keep her from reading his notes. On the way to NERV, Rei asked him a question that he didn't know how to answer. 

"Pilot Ikari do you love me?" Rei asked looking at him. 

"I...do not know, I think I have feelings for you but I don't know what they are as of yet." Shinji answered. 

"I see, I believe I feel the same way. As soon as I figure these feelings out I will inform you." Rei said. 

"I see." Shinji said, expressionless on the outside but... couldn't figure out how he felt on the inside. 

"Well it's about time, it's not like you two to be late, did you have trouble?" Ritsuko asked as she readied Shinji for a test, or so it seemed. 

"I am going to implant you with these." said the Dr., as she showed him the implant. The implant looked like a paper-thin curving metal plate with a plug on one side, and various wires on the other side. 

"What is its purpose?" Shinji asked, while Ritsuko put the implant on the table. 

"It allows us to store your memories on a computer." She explained. Ritsuko injected Shinji with a sedative, and about two minutes later Shinji was out. "I hope I am doing the right thing, Gendo." Ritsuko said, as she started the operation. About two hours after the operation, Shinji woke up. He had a throbbing headache, but all in all he felt pretty good, thanks to the sedative that Ritsuko gave him. 

"Ah, you are awake." Shinji couldn't remember that voice at first, but it came to him a second later. 

"Fath... commander Ikari, what do you want of me?" Shinji asked trying to pull off his usual monotone voice, but it came out as a weak whisper. Surprised, he slowly grasped his throat. 

"It's alright, the implant reroutes all of your actions through it as well as record your memories," Gendo explained, "it will return to normal in an hour or two. Don't worry, it will be over soon, we only have one more procedure to do and you will be ready." 

A nurse came in the next day and gave him a shot like the one that Ritsuko had given him the day before, and fell asleep once more. This time when he woke up, he felt different somehow. He felt like someone else was inside him, not controlling him, but just sleeping there. It scared him a little. 

"So, how is my little patient?" Ritsuko asked. 

"I feel...I feel like someone is inside of me." Shinji said. 

"That is natural, you will come to ignore it in time." Rei chimed in as she walked in from the door. 

"You knew of this? Why didn't you tell me of this." Ritsuko asked, slightly annoyed at the younger pilot for not keeping her in the loop. 

"What do you mean?" Shinji asked. 

"You have been injected with the first angel's genes, in short you and Rei are brother and sister in the fact that both you and she have 25% Gendo's DNA, 25% anonymous DNA and Shinji has 50% Adam's DNA while Rei has 50% Lilith's DNA." Ritsuko explained. 

"Why are you telling us this?" Rei asked. 

"I unlike your 'father' like to be out in the open with people." She said. Both Shinji and Rei cocked an eyebrow. Ritsuko shuddered. "Don't do that. You two have sure inherited some of his worse traits." Ritsuko said after her shuddering fit. 

"I still do not understand, you are telling us this information and we do not know. Why." Shinji inquired, neither one of them willing to give up. 

"Because Gendo wants to use you as he was using me. I used to do anything he asked just for his affection, and in turn I helped kill people. I don't want you to make the same mistake." Ritsuko said looking sincere. 

"Then we will take that in to consideration when we make our choices." Shinji answered. That was good enough for Ritsuko. 

"What will I tell Captain Katsuragi?" Shinji asked, pointing to his head, which was now a mix of very dark blue and brunette, with light blue highlights. 

"She was told that there was a problem with the tests and that you were admitted in here for safety precautions. But now we have a bigger test, we have to find out how much this will affect your ability to pilot EVA." Ritsuko said taking on her scientist's voice. 

END CHAPTER FIVE: REALIZATIONS

A.n.: How's that for a twist huh? As said I am going to make spin-offs for the other women as well but I still haven't decided how to make the main one. I am thinking very hard about a Misato / Shinji as well, but I will need some help. Oh and I am sorry for these chapters being so long, I just don't know when to quit. Well I have had a good day, I have finished another very long chapter and I haven't been interrupted yet. Well I am going to get started on another chapter, after I clean out my closet and stuff. Well I'm 10-7


	6. a new room mate

CHAPTER SIX: A NEW ROOMMATE

DISCLAIMER: I own nothing that relates to Evangelion, except Kell, who is not worth mentioning.

'-------------' =thoughts

"------------"= speech

(-------------)= me interrupting your reading for a side note

"Shiiiin-kuuuun, we have somewhere, to go. Are you up?" Misato asked as she walked in to Shinji's room. Misato was told that his eye and hair color change was due to the accident. Shinji's eyes were now ice blue instead of their usual deep blue, and his hair was now a very dark brown with moderate blue highlights. "Shinji? Are you alright?" Misato asked as she waved a hand in front of his face. 

"Huh? Oh, I am fine." Shinji said, obviously lying, but he could not tell anyone. 

"Well, you and I have some things to do today. We have to pick up a new roommate. Her name is Asuka. She is also an Evangelion pilot." Misato said, looking eerily cheery this morning. 

"Why am I needed?" Shinji asked. The presence hadn't gone away, but it wasn't bothering him anymore either. 

"Because, I don't feel like leaving you alone. You have been acting more withdrawn than usual lately." Misato answered. 

"I understand." Shinji answered. Shinji wanted to talk to Misato about what was going on, but remembered what Commander Ikari said to him. 

On the way to the Train station, Shinji started to feel the presence get stronger. "An angel." Shinji whispered, causing Misato to look all around. Just then the pilots cell went off. He heard the automated message, and then he and Misato went to NERV to prepare for the upcoming battle. Once they got to the command HQ, they parted company for awhile. After Shinji got changed into his plug suit, he walked to the briefing room. On the way, he ran into Rei walking there as well. 

"Excuse me, pilot Ayanami, may I talk to you?" Shinji asked. 

"I know what you are feeling, I feel it to, although it has never been this strong." Rei said, answering his question, as they entered briefing room. After they were briefed on the situation, the two pilots got into their respective entry plugs and were inserted into the Evas. When the Evas were on the surface, they waited for the angel to attack. While they were waiting, Shinji opened a secure Comm link with Rei. 

"The feeling is getting very intense, what should I do?" Shinji asked, looking a little out of breath. 

"I am not sure, this has never happened to me." Rei said, also looking a little out of breath. Just then, the angel swooped down and rammed unit one. Unit one went through one building and into another. Before either Shinji or Rei could react, the angel grabbed unit one with one of its feelers, and threw it at Unit Zero. 

"Both units have received minor damage to external armor, but are still fully operational." Makoto reported. Unit One got up and charged. The angel threw one of its feelers at Shinji and missed, but it cut his power cable. That knocked Shinji off balance with the sudden loss of weight. The angel took that moment to grab Shinji again and threw him towards the mountains, and turned on Rei. 

Shinji was about to get up, when he noticed the two people that had been hanging around him. "Captain Katsuragi, there are civilians on the battleground. What do you want me to do?" Shinji asked. He didn't have time to get an answer as the angel threw a feeler at unit one. Shinji caught it in his hand, but didn't fight; he was still waiting on his orders. He looked at where it and unit zero were fighting and saw that unit zero was out of the battle. Shinji started to wince as the feelers started to burn his Eva's hand.

"Have Unit One hold with its current orders and eject the plug and let the boys in." Misato ordered. 

"Captain, that will significantly decrease my synch ratio with unit one." Shinji informed. 

"I know, you are to escape using route 35." Misato answered. Shinji did as ordered at first, he let the two civilians in the plug. When the Eva got back on it's feet it, instead of trying to get away, he got it's progressive knife out with it's free hand, and slashed the feeler in two. The angel reared back in pain and Shinji took the opportunity that presented itself and started slashing the red core and soon, about thirty seconds before his reserve power ran out he defeated the angel. 'What is this feeling? Am I sad because I took the life of something similar to myself?' Shinji thought as unit one's power finally ran out. 

"Why did you disobey a direct order?" Misato questioned, as she tapped her finger on the table, waiting for an answer. 

"I was ordered by you, to take any opportunity given to destroy the enemy I did so. You made no order to take the civilians safety into account." Shinji said. 

"He is right, Captain Katsuragi, you did order us to take any steps necessary to take out the enemy. Do you not remember the briefing?" Rei asked, with an arm in a sling. 

"What ever, Shinji, I want you to meet me at the car in thirty minutes, we still have an errand to take care of." Misato said as she left the two young pilots to themselves. 

"I will see you later then, to continue our conversations." Shinji said as he left the room also. Shinji made it to the car and was waiting for Misato. 

"Sorry I'm late, I had some last minute things to do." Misato said as she unlocked her door. 

"It is of no concern to me." Shinji said, as he got in the car. They actually made it to the train station without any problems this time, and on time to boot. Misato had planned on getting there early. 

"Is this the platform she is supposed to come on?" Shinji asked as he stared off in space. 

"Yes, why do you ask?" Misato asked as she looked on at the oncoming train, only to be ignored by her charge. The train itself was slow, as it looked as if it had a heavy load on one of its cars. The car behind the freight car looked like a fancy looking passenger car. When the train stopped, the passenger car was a little ways of from where Misato and Shinji were standing. The duo walked over the car, and were met by a middle aged man, about the same age as Misato, and a girl with long red hair, held up by what seemed to be the A-10 connectors to a plugsuit. 

"I am pilot Ikari, Shinji. Myself and Captain Katsuragi are to escort you to NERV headquarters." Shinji said, still void of emotion. 

"Wow, a real firecracker isn't he?" the girl said, smirking. "I am the great Asuka Langley Soryu, third children, and you are the famous second child, I know who you are, I'm surprised you do not know who I am." the girl exclaimed. 

"Hey, Asuka, you aren't going to say hey to me? Not even a hug?" Misato asked, tapping her foot. 

"I'm too old for that now, isn't that right Kaji." Asuka said as she crossed her arms. 

"I do not mean to interrupt, but may we please hurry, I have a prior engagement to attend to." Shinji said, remembering that Dr. Akagi-san wanted him to come in to the office to run some tests to see how he was doing with the new implant. 

"And what is this prior engagement?" Misato-san asked. "It is classified, and you do not have the clearance for me to tell you." Shinji answered. 

"As your commanding officer, I demand you to tell me." Misato-san said, starting to get annoyed, added that to the fact that her stock of hidden beer had run out, and you have one very irritated woman. 

"If you have any objections, take it up with Commander Ikari, not me." Shinji said, becoming even more monotonous than before. 

"I think he acts like a doll." Asuka said, making a disgusted face. 

"Well, Asuka, I guess someone from NERV will have to bring your things over, seeing that we have to leave." Misato said, shooting an evil look that would make the fiercest animal shudder, but didn't affect the second children. 

"Captain, we really have to go, I am needed at NERV." Shinji said as he sat down in the back of Misato's car. 

"Oh well, I guess we can talk while we wait on him." Misato-san said as she shrugged and walked to the car, with Asuka following closely, asking what was going on. The man known as Kaji, was just standing there, looking confused, then realized he was being left, quickly started chasing after the car. 

After they finally got to the NERV HQ, Shinji informed them that he would be home after while and for them to go on. 

"You wanted to see me after Captain Katsuragi-san got through with her errands?" Shinji asked after he entered Dr. Akagi-san's office. 

"Yes, please lay on that gunnery." Ritsuko ordered. 

"Hai." Shinji said as he laid down on the gunnery. Well it was not an actual gunnery, because it had a headrest that revealed his neck. Ritsuko attached the necessary instruments to the implant that they had put in him, during the last operation, after he laid on the gunnery. It was barely noticeable, but there were two small plug interfaces right at the edge of his hairline, and one about a quarter of an inch above the other two. The three jacks looked like a triangle. She inserted three plugs, to download his memories and data that the implant had taken. 

"In just a minute you will have completed your first memory download. You will be rendered unconscious during this time, so do not be alarmed." Ritsuko said as she typed on her keyboard. A few seconds later, Shinji's vision started to blur, and he had trouble comprehending his surrounding, and soon phased into a deep sleep. About two hours later, he woke up. 

"Was the memory dump a success?" Shinji asked as he looked around for Dr. Akagi-san. 

"It was." she answered from behind his gunnery, as she looked at him, removing the plugs from his interface objects. 

"I see." Shinji said as he looked at his watch, that Misato had recently bought him. "Captain Katsuragi-san, will be angry at me." Shinji stated. 

"What about?" Ritsuko-san asked, as she helped him up. 

"It is past my designated time to be at her apartment." Shinji said, still disoriented from the memory dump. 

"What? Just tell her that I kept you here, for further tests." the doctor. suggested. 

"Understood." Shinji said as he finally stayed standing without help. 

"I have to do this two times a week?" Shinji asked as he turned, to look at his physician. 

"Yes, I am afraid so, although you will get used to it." Ritsuko-san stated coolly.

"One more thing, I am having unsure feelings about this new girl that is to live with us, she may be...troublesome." Shinji said, still as expressionless as ever. 

To his and Ritsuko-san's surprise Gendo answered, from the door to the lab. "We can try increasing your dosage, to see if that will work for you, Shinji." 

"Yes, that will be sufficient." Shinji said as he cautiously walked over there, still feeling a little woozy from his first dump. 

"If this doesn't work, I will assign you to live at Dr. Akagi's place of residence. Give it two weeks, then report directly to me." Gendo ordered, causing Ritsuko-san to jerk her head up. 

"Excuse me?" Ritsuko-san asked, visibly flabbergasted. (Couldn't find a better word.) 

"Yes, Ritsuko?" Gendo asked, waving for Shinji to leave. 

"What in the name of Kami are you doing?" Ritsuko-san asked after she was sure that Shinji was gone. 

"I am making sure that neither of you slip up, as soon as he reports to me, if need be, I will send him to you and have him report anything you do that he thinks is suspicious behavior." Gendo said as he started walking out the door. 

"What makes you think I am acting suspicious?" Ritsuko-san asked. 

"Let's just say, I've got my reasons." Gendo said, 

"Oh, and I'll be expecting you at my office after you finish up. 'That is the only thing I enjoy from you.' Ritsuko-san thought as she sort of brightened a little, at the thought. 

On the way to Misato's apartment, he stopped at one of the grassy hills and sat down, deciding to take advantage of Ritsuko-san's excuse. "Excuse me, may I sit here too?" asked a voice that sounded familiar to him. He turned to look at the person and found the German girl that he and Misato picked up earlier. 

"Yes, you may." Shinji answered, in his usual emotionless voice. 

"I have a question, if you don't mind answering." the German girl known as Asuka said. 

"I don't." Shinji answered, still in his unattached voice. 

"Why weren't you impressed by me at the train station? Most males flock around me when they see me. All you did was introduce your self." Asuka said as she stared at him. Shinji turned to her, causing her to make eye contact. She was mesmerized and frightened at the same time. On the one hand he had the most unusual and beautiful eyes she had ever seen, and yet they were lifeless. 

"You are just another pilot. I do not know how other males act around you, or why they act as they do, all I know, is what commander Ikari tells me." Shinji said as he looked away, suddenly going pale. 'What is this feeling? Could there be something wrong with me? There couldn't be, I just left from Dr. Akagi-san's office, and she mentioned nothing.' Shinji thought. "I-I must leave, n-now." Shinji said, slowly getting up, sort of stumbling off the hill, gasping like he was out of breath. 'What is this?' Shinji thought as he started having trouble staying conscious. A few seconds later the feeling slowly went away. 

"Hey! Wait for me!" Asuka shouted, chasing Shinji, after watching him.

END CHAPTER SIX: A NEW ROOMMATE

Author's notes: well I still haven't figured out whom to pair together. I think I might go with a Shinji/Asuka, but I might surprise you with something else. Well I got to go, it's two in the morning again, and I have to get up at 5:30 to watch Zoids: chaotic century. I'm 10-7 for now.

update: 11/17/02 Thanks to Raziel the damned for prereading all of my chapters so far, and for being co author. 


	7. Part of chap 7: Rain

PART OF CHAPTER SEVEN: RAIN

                The next day, Shinji did his usual routine of getting up, fixing breakfast, getting ready for school, and studying a book. Although, something was different, he looked like he didn't get enough sleep.

"Man! It hasn't stopped raining since you and Asuka got back." Misato mumbled as she trudged over to the fridge and took out a beer. Misato had actually talked Gendo into letting her have her beer back. 'think you can take my beer away, do you?' Misato thought as she stuck her toungue out at the boy. Misato went and sat down near Shinji, and instead of gulping her beer, she only took regular swallows.

"Shinji, I need you to do something for me, lt. Ibuki needs some help with stuff today, so I need you to help her, at NERV." Misato said before taking another swallow of her beer.

"What about school?" Shinji asked as he set the book down on the coucharm.

"It's been cleared with school." Misato answered.

"Hai." Shinji said as he got up and went to change out of his school clothes and into the NERV tech uniform that Misato had given him. It was similiar to the one that lt. Ibuki wore, but this one was black with yellow trim, instead of the white with pink trim, or the kind with blue trim.

"This uniform let's the other techs know that you are one of the pilots, and not just another tech." Misato said as she watched him sit down on the couch.

"I understand, but I would like to know what excactly I will be helping lt. Ibuki with." Shinji said, looking at the rain sliding down the door of their balcony.

"You will be helping her input information into the MAGI supercomputers, and whatever else she needs help with." Misato continued. 

"How do you people get up so early?" came a voice with a german accent, from the third room, then came a scantily clad girl out of the room. She had a shirt that barely covered her small cleavage, and nothing but underware on, on the bottom.

"My, are you going to wear that around Shinji?" Misato said, in a mock good girl attitude.

"Stuff it." came the reply.

"I will be on my way, Misato-san." Shinji said, as he got his keycard off of the table, and walked to the door.

"Do you want me to give you a ride?" Misato asked, going for her raincoat.

"No, I will be fine." came the answer followed by a shutting door.

"I still say he acts like a doll, so cold, no emotion at all. It's freaky." Asuka said, shivering.

"I don't know what's going on yet, but his father is doing something to him." Misato said under her breath. Over the next two weeks, Asuka had gotten settled in, and started harrassing Shinji, to the point that he nearly lost his temper.

On the day that he was to report to Commander Ikari, he had made a report of all the 'going ons' over the past two weeks. He was not pleased to see the reports. "Pilot Ikari, you are to report to this address after you get off today." Gendo said as he handed Shinji a piece of paper, with an address.

"Hai." came the response.

"You may return to assisting lt. Ibuki." Gendo said, waving him off.

))))))))

"Well, what did he want?" Maya asked, as she and Shinji carried a bunch of files to the computer room to put them on the computer.

"Why do you ask?" Shinji asked, as an answer.

"Because, I'm curious, that's all." came the reply

"I can not tell you that." Shinji said as he slipped his NERV key card through the slot, and entered the room.

"I am only trying to start a conversation, you don't have to bite my head off." Maya said, getting a little aggravated. Shinji seemed to ignore her. "You know, I've noticed that you have taken to sempai, why is that?" Maya asked, still trying to strike up some small talk.

That seemed to hit a nerve in Shinji. "I...I don't...I don't know." Shinji whipered, suddenly looking out of breath, and then falling to the floor, shaking a little bit.

"OH,KAMI!" Maya screamed as she ran to the violently shaking boy.

"Something is counteracting the adam cells that we have with fused his body." Ritsuko-san said as she looked at the boy who had stopped convulsing, but was still in bad shape. "Shinji, we are going to perform another memory dump, just in case we have to...Revive you." Ritsuko-san said as she plugged the machine into to Shinji. "I will not make it." Shinji said as Ritsuko-san started the last memory dump for Shinji-I.

I thought that since I'm still in the middle of a bad case of writer's block, I would take the time to reply to the posts that I seem to have neglected.

Sougen-san :  I really appreciate your praise, I'm not sure about the pairings as of yet, but who knows? I am honored to even be compared to Random1377.

Priest :  I'll take the announcement thing into consideration, I know how aggravating it can get to think there's another chapter and it's an announcement.

Josh Maxwell :  There ARE very few good R/S stories out there aren't there? Well I'm not sure about the pairings as of yet, and if there are any innuendos in the story already, it can be explained as non-understanding of their/his/her emotions.

Xardion :  I thank you for your sympathy, but mistakes happen, and I made one. Oh well, live and learn, huh?

???????????? :  Oh well, can't be perfect all the time! Lol

Phoenix :  I appreciate your review, and hope you keep reading, when I can get another chapter out.

Scsim :  I haven't really thought about who Rei's mother is(have to check over notes later to make sure though) but the pairing would work, although as I said to the others the pairings are as of yet undecided. I might take a poll to see what the ppl think.

Daniel :  thanks for you words of confidence(you know, there's only so many ways you can say the same thing different ways). I'm thinking about a poll, and I have taken your suggestion to heart in the later chapters in the story, and am about to revise the early chapters.

Zentrodie :  Considering so few ppl use it, yeah it is unique. Another unique take on this type is Professor A. Pendragon's story "Neon Exodus Evangelion"

Sinnatious :  I wouldn't do something like that, would I? (whistle's innocently) lol. I might, if it helps the story's plot some.Besides, this is NGE we're talking about, it's all about death and rebirth and such. I think. Maybe. Thanks for the review!

Dennisud :  Yeah I see what you're talking about. I may have to revamp some chapters because of that, or like I said above; downplay it on the grounds of  their lack of understanding of emotions. Thanks for reminding me about Assuka's attitude (heh, heh, I made a funny).

Kale :  see aove on the pairings, heheh, I might just make them room mates, or something.

Hyperion :  True, it wouldn't really be incest. I hadn't really thought that far ahead yet, but that's always a good idea.

Damerei A :  Thanks for the comment, and your write, most ppl don't really think about alternate reality fics like this often.

JD :  thanks for the review, I'll try to keep up the good work. Although it's slow going.

Raziel The Damned :  I really appreciate the praise, even though you seem to have dropped off the map.

Thanks for all the reviews, to everybody that reviewed.

I'm sorry about not updating in a long time, but well, you know how life and writers block are.

Here's a Poll: Which pairing would you like to see?

Rei / Shinji

Asuka / Shinji

Maya / Shinji

Ritsuko / Shinji

Misato / Shinji


	8. possibly a new chappy

Here's one way the story could've taken a turn.

Again, I apologize about being so late at reviewing, but not too long after I posted part of the chapter 7, my laptop died a tragic death!(hard disk corrupted somehow) Anyhoo, all my notes and stuff were on it and I've had to read each of the chapters, and try to remember what I was thinking at the time I wrote them.(not an easy feat if you knew me! lol.)

CHAPTER EIGHT : INDECISION

DISCLAIMER: I own no one in this story as of yet, all the original characters of the series, anime, manga, movies, belong to GAINAX and the original creator of the series.

"I have not determined the cause of this particular problem as of yet, although I have reason to believe it was the meds you have put him on." Ritsuko-san told the commander as she stood in front of his desk, reading out the reports so far.

"And what of the others? What do they know of this situation?" asked the ever calm commander.

"They believe he was sent to another NERV facility. His thought patterns are currently in memory storage at the moment. Though there is a problem. It seems that finding the cause of this problem in Shinji is going to take an extended amount of time, and with something as complicated as a person's thought patterns in a computer…" Ritsuko-san trailed off.

"That it would most likely erode, or waste away. Or even worse yet, someone might be able to hack the system. We've had problems with minor hackers for the last couple of years. Although the targets have been non-consequential areas, up until now, I will not take that risk. Take his thought patterns and insert them into one of the spare Rei clones." Gendo said as he rose from his seat. Come, have lunch with me." Gendo said, his tone more of a command than a request.

"I have…" Ritsuko started, but couldn't finish under Gendo's glare, and meekly nodded her assent. Soon they were on their way to the mess hall. While on the way, Gendo asked the good doctor a question: "What reason would you have to try to sway Rei and Shinji?"

Meh, if you have to blame something blame all the Ranma .5 fics I've been reading. Just remember though, that this is only one of the ways that this story could go, and your reviews will ALL be taken into consideration.

Here's a poll on who the readers think the pairings should be.(current results are taken from past reviews.) I'll add on characters that GET votes as I get them.

**_Normal (sort of)_**

Rei - 4

Asuka - 2

Maya - 3

**_Weird_**

Ritsuko-san - 2

No-one - (believe it or not) 1

Ja ne

P. S. - To try to remedy a problem with people who are new to the fanfiction world and don't have a firm grasp on the randomly strewn about Japanese words in them here is the most common ones I've found.

**_Gomen_** – sorry

**_Iie_** – no

**_Ite_** – ow/ouch

**_Baka_** – stupid/idiot

**_Hai_** – yes

**_Sempai_** – upperclassman/ someone you look up to

????**_-san_** - sign of respect

If you find words in this story you don't understand then include them in your review/flame and I'll take care of the problem post-haste(which for me is a couple days later)


End file.
